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X-ray structure of Danio rerio histone deacetylase 6 (HDAC6) CD2 in complex with a inhibitor SS555
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5EEK
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5.5 283 0.1 M Bis Tris, 0,2 M KSCN, 16% PEG 3350
Protein stock buffer: 5% DMSO, 0.004M SS555, 0.05 M Hepes pH 7.5, 0.001M TCEP, 5% v/v glycerol, 0.1M KCl
Crystal Properties Matthews coefficient Solvent content 2.4336634 49.490314
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 54.809 α = 90 b = 83.811 β = 97.971 c = 86.092 γ = 90
Symmetry Space Group P 1 21 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 PIXEL DECTRIS PILATUS3 2M 2019-01-16 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON BESSY BEAMLINE 14.2 0.9184 BESSY 14.2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Net I Over Average Sigma (I) Redundancy Number Reflections (All) Number Reflections (Observed) Observed Criterion Sigma (F) Observed Criterion Sigma (I) B (Isotropic) From Wilson Plot 1 1.6 85.26 98.8 0.151 0.179 0.095 0.994 6.5 6.7 100361 12.16
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.6 1.63 99.6 1.056 1.27 0.693 0.612 1.3 6.4
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 5eek 1.6 54.34 -3 99303 4983 98.8 0.192 0.191 0.2032 0.23 0.213 Random selection 15
Temperature Factor Modeling Anisotropic B[1][1] Anisotropic B[1][2] Anisotropic B[1][3] Anisotropic B[2][2] Anisotropic B[2][3] Anisotropic B[3][3]
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5580 Nucleic Acid Atoms Solvent Atoms 758 Heterogen Atoms 117
Software Software Software Name Purpose REFMAC refinement DIALS data reduction DIALS data scaling PHASER phasing